Genome Analysis Toolkit

Variant Discovery in High-Throughput Sequencing Data

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Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery
and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size.
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Category
Variant Annotations

Overview

Output consists of two three-element arrays. The elements of SA_POST_PROB are, respectively, the posterior probabilities that there exists an artifact on the forward strand, an artifact on the reverse strand, or no artifact.
These probabilities are normalized to sum to 1. The elements of SA_MAP_AF are the max a posteriori estimates of the variant allele fraction given a
forward strand artifact, a reverse strand artifact, and no artifact, respectively. For example SA_POST_PROB = 0.9, 0.02, 0.08 and
SA_MAP_AF = 0.01, 0.1, 0.2 together mean that the apparent variant is most likely a forward strand artifact, but if it is actually a true
variant its allele fraction is most likely 0.2.